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| Status |
Public on Jul 01, 2017 |
| Title |
mut_unt_meDIPSeq |
| Sample type |
SRA |
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| Source name |
HOXA9 IDH1 R132H
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| Organism |
Mus musculus |
| Characteristics |
cell type: HOXA9 immortalized bone marrow
treatment: Untreated
vector genotype: IDH1 R132H
chip antibody: Anti-5-methylcytidine (Eurogentec; Catalogue:BI-MECY-0100)
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| Treatment protocol |
For vitamin C treated samples, daily addition (0h, 24h, 48h) of vitamin C to a final concentration of 0.345mM before harvesting at 72h after the first treatment
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| Growth protocol |
Cells were plated at a density of 5x105 cells/ml in 4mL DMEM medium (Stem Cell Technologies, Vancouver, Canada) supplemented with 10% heat inactivated fetal bovine serum (Life Technologies) and 6 ng/ml murine IL-3, 10 ng/ml human IL-6, and 20 ng/ml murine SCF (Peprotech, Hamburg, Germany).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was sonicated to approximately 200–400 bp with a Covaris E-220 Sonicator (Covaris) and end-repaired using standard Illumina library preparation protocol. DNA was immunoprecipitated with anti-5-methylcytidine antibody. Immunoabsorbed DNA fragments were recovered by adding a rabbit anti-mouse IgG secondary antibody (2.5 mg/ml, Jackson ImmunoResearch) and incubating for 2h. To complete library preparation, the immuno-precipitated DNA was purified and subjected to two 10-cycle PCR reactions using 16 μl of DNA for each sample with paired-end Illumina PCR primers. A final size selection was performed to select all fragments <700 bp in size by electrophoresis in 8% polyacrylamide gel.
Genomic DNA/RNA was extracted using the Qiagen AllPrep Mini Kit according to the manufacturer's instructions.
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| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Base-calling was performed using CASAVA 1.8.2 on the HiSeq 2500 platform
Alignment to mm10 was performed by bwa (bwa-aln) version 0.5.7
Wig tracks were generated from bam through in-house tools using ChIP-Seq mode with SAMtools (v0.1.16) flags "-F 1028 -q 5"
A custom java program (bamToWig) was used to generate wig files for downstream analysis and visualization. Reads with BWA mapping quality scores <5 were discarded and reads that aligned to the same genomic coordinate were counted only once in the profile generation.
Pairwise, differential peaks between wild-type, mutant, untreated and vitamin C treated samples (DMRs) were called using MACS (macs14 1.4.2) with a threshold pe-5 and the MEDIPS R package (p<0.05)
Chastity failed reads were flagged using in-house tools
Duplicate reads were marked using Picard Tools' MarkDuplicates.jar (version 1.71)
Wig tracks were generated from bam through in-house tools using ChIP-Seq mode with SAMtools (v0.1.16) flags "-F 1028 -q 5"
Genome_build: mm10
Supplementary_files_format_and_content: mut_iMR_medip.bed: regions gaining methylation in untreated IDH1mut compared to untreated IDH1wt from meDIP-seq data
Supplementary_files_format_and_content: deMR_medip.bed: regions losing methylation upon vitamin C treatment in IDH1mut from meDIP-seq data
Supplementary_files_format_and_content: iMR_medip.bed: regions gaining methylation upon vitamin C treatment in IDH1mut from meDIP-seq data
Supplementary_files_format_and_content: iHR_medip.bed: regions gaining hydroxy-methylation upon vitamin C treatment in IDH1mut from hmeDIP-seq data
Supplementary_files_format_and_content: H3K4me1_unt.bed: peak coordinates, -log10(q) and peak width for H3K4me1 untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K4me1_vitc.bed: peak coordinates, -log10(q) and peak width for H3K4me1 vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K4me3_unt.bed: peak coordinates, -log10(q) and peak width for H3K4me3 untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K4me3_vitc.bed: peak coordinates, -log10(q) and peak width for H3K4me3 vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K27ac_unt.bed: peak coordinates, -log10(q) and peak width for H3K27ac untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: H3K27ac_vitc.bed: peak coordinates, -log10(q) and peak width for H3K27ac vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: pu1_unt.bed: peak coordinates, -log10(q) and peak width for pu1 untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: pu1_vitc.bed: peak coordinates, -log10(q) and peak width for pu1 vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: runx1_unt.bed: peak coordinates, -log10(q) and peak width for runx1 untreated chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: runx1_vitc.bed: peak coordinates, -log10(q) and peak width for runx1 vitamin C chIP-seq from MACS2 (q<1e-5)
Supplementary_files_format_and_content: mut_unt_RNAseq_pc_rpkm: rpkm values for IDH1mut untreated RNA-seq where columns are as described (http://www.epigenomes.ca/data/CEMT/analysis/readme/file_formats.html)
Supplementary_files_format_and_content: mut_vitc_RNAseq_pc_rpkm: rpkm values for IDH1mut vitaminC RNA-seq where columns are as described (http://www.epigenomes.ca/data/CEMT/analysis/readme/file_formats.html)
Supplementary_files_format_and_content: vitc_downregulated_genes.txt: For genes down-regulated by vitamin C; Gene Name and Ensembl id (mm10 v71)
Supplementary_files_format_and_content: vitc_upregulated_genes.txt: For genes up-regulated by vitamin C; Gene Name and Ensembl id (mm10 v71)
Supplementary_files_format_and_content: iMR_wgbs.bed: regions gaining methylation upon vitamin C treatment in IDH1mut from WGBS data
Supplementary_files_format_and_content: deMR_wgbs.bed: regions losing methylation upon vitamin C treatment in IDH1mut from WGBS data
Supplementary_files_format_and_content: ctrl_unt.q5.F1028.PET.wig: wt_unt_meDIPSeq wig file
Supplementary_files_format_and_content: ctrl_vitc.q5.F1028.PET.wig: wt_vitc_meDIPSeq wig file
Supplementary_files_format_and_content: mut_unt.q5.F1028.PET.wig: mut_unt_meDIPSeq wig file
Supplementary_files_format_and_content: mut_vitc.q5.F1028.PET.wig: mut_vitc_meDIPSeq wig file
Supplementary_files_format_and_content: muthmedip_unt.q5.F1028.PET.wig: mut_unt_hmeDIPSeq wig file
Supplementary_files_format_and_content: muthmedip_vitc.q5.F1028.PET.wig: mut_vitc_hmeDIPSeq wig file
Supplementary_files_format_and_content: H3K4me1_unt.q5.F1028.PET.wig: mut_unt_H3K4me1 wig file
Supplementary_files_format_and_content: H3K4me1_vitc.q5.F1028.PET.wig: mut_vitc_H3K4me1 wig file
Supplementary_files_format_and_content: H3K4me3_unt.q5.F1028.PET.wig: mut_unt_H3K4me3 wig file
Supplementary_files_format_and_content: H3K4me3_vitc.q5.F1028.PET.wig: mut_vitc_H3K4me3 wig file
Supplementary_files_format_and_content: H3K27ac_unt.q5.F1028.PET.wig: mut_unt_H3K27ac wig file
Supplementary_files_format_and_content: H3K27ac_vitc.q5.F1028.PET.wig: mut_vitc_H3K27ac wig file
Supplementary_files_format_and_content: input_unt.q5.F1028.PET.wig: mut_unt_hchip_input wig file
Supplementary_files_format_and_content: input_vitc.q5.F1028.PET.wig: mut_vitc_hchip_input wig file
Supplementary_files_format_and_content: pu1_unt.q5.F1028.PET.wig: mut_unt_pu1 wig file
Supplementary_files_format_and_content: pu1_vitc.q5.F1028.PET.wig: mut_vitc_pu1 wig file
Supplementary_files_format_and_content: runx1_unt.q5.F1028.PET.wig: mut_unt_runx1 wig file
Supplementary_files_format_and_content: runx1_vitc.q5.F1028.PET.wig: mut_vitc_runx1 wig file
Supplementary_files_format_and_content: Input-untreated_tfchip.q5.F1028.PET.wig: mut_unt_tfchip_input wig file
Supplementary_files_format_and_content: Input-VitC_tfchip.q5.F1028.PET.wig: mut_vitc_tfchip_input wig file
Supplementary_files_format_and_content: IDH1mut-VitC-1.q0.F516.neg.wig: IDH1mut_rnaSeq untreated negative strand wig file
Supplementary_files_format_and_content: IDH1mut-VitC-1.q0.F516.pos.wig: IDH1mut_rnaSeq untreated positive strand wig file
Supplementary_files_format_and_content: IDH1mut-untreated-1.q0.F516.neg.wig: IDH1mut_rnaSeq vitamin C treated negative strand wig file
Supplementary_files_format_and_content: IDH1mut-untreated-1.q0.F516.pos.wig: IDH1mut_rnaSeq vitamin C treated positive strand wig file
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| Submission date |
Oct 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Martin Hirst |
| E-mail(s) |
mhirst@bcgsc.ca
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| Phone |
604-822-6373
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| Organization name |
University of British Columbia
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| Department |
Department of Microbiology & Immunology
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| Street address |
2125 East Mall
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| City |
Vancouver |
| State/province |
British Columbia |
| ZIP/Postal code |
V6T 1Z4 |
| Country |
Canada |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE87623 |
Vitamin C induced epigenomic remodeling in IDH1 mutant acute myeloid leukemia |
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| Relations |
| BioSample |
SAMN05862242 |
| SRA |
SRX2210942 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2335664_deMR_medip.bed.gz |
26.8 Kb |
(ftp)(http) |
BED |
| GSM2335664_mut_unt.q5.F1028.PET.wig.gz |
61.0 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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